The presence of contaminants of emerging concern (CECs) in wastewater effluent and surface waters is an important field of research for analytical scientists. This study takes a suspect screening approach to wastewater and surface water analysis using comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (GC × GC-TOFMS). Two extraction procedures, traditional liquid–liquid extraction (LLE) and stir bar sorptive extraction (SBSE), were utilized and evaluated for their application to wastewater and surface water samples. Both techniques were evaluated regarding their recovery rates, range of compound classes extracted, and on their application to discovery of CECs. For the 14 surrogate compounds analyzed, LLE was able to extract all of them in each matrix with a recovery range of 19% to 159% and a median value of 74%. For SBSE, the recovery rates ranged from 19% to 117% with the median value at 66%, but only 8 of the compounds were able to be extracted because of the polarity bias for this extraction method. A new method of SBSE calibration was also developed using direct liquid injection of the internal standards before desorption of the stir bars. Initial findings indicate increased sensitivity and a greater range of unknown analyte recovery for SBSE, especially in the more dilute effluent and surface water samples. With the methods used in this study, SBSE has a concentration factor of approximately 416, improving that of LLE, which is 267. Suspect screening analysis was utilized to tentatively identify 32 CECs in the samples, the majority of which were pharmaceuticals and personal care products. More CECs were found using SBSE than LLE, especially in the surface water samples where 13 CECs were tentatively identified in the SBSE samples compared to 6 in the LLE samples.